A High-Level Language for Rule-Based Modelling

摘要: Rule-based languages such as Kappa excel in their support for handling the combinatorial complexities prevalent many biological systems, including signalling pathways. But provides little structure organising rules, and large models can therefore be hard to read maintain. This paper introduces a high-level, modular extension of called LBS-κ. We demonstrate constructs language through examples three case studies: chemotaxis switch ring, MAPK cascade, an insulin pathway. then provide formal definition LBS-κ abstract syntax translation plain Kappa. The is implemented compiler tool which available web application. finally how increase expressivity embedded scripts general-purpose programming language, technique we view generally applicable other domain specific languages.